If the player gets their hands on a planet destroying super weapon it would be very unsatisfying if they destroy a world to find it magically reappear when they reload, or even just visit the next solar system and come back. These changes need to be saved permanently to the players save data.
I'm planning for save data to be like a patch that is applied over the top of the procedurally generated data. So if you kill someone when it comes to generate their info when it's finished it will stamp 'dead' over the top of their status. It will maybe go on to generate different things off the back of this, maybe give them a grave or something. A planet will be patched with 'exploded' and perhaps an asteroid field will get generated.
This approach will require that the generation algorithms be exactly the same as when the patch data was created. So save games will not survive updates to the game that change these. They will need to be bound to a release version and people should complete their adventures before upgrading, if they want. Not sure if there's an elegant way around that.